[maker-devel] CDS retrieve from augustus_masked

[Kang, Yang Jae]

Thank for your quick response Mike

I looked the file named transcript, but it might include UTRs I suspect. What I want to do is calculating Ka Ks values so that I need coding sequences. Is there any indication where is exact START and STOP in the transcript file? 

 

Thank you

 

 

From: Michael Thon [mailto:mike.thon at gmail.com] 
Sent: Saturday, April 06, 2013 8:20 PM
To: Kang, Yang Jae
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] CDS retrieve from augustus_masked

 

Hi Kang - After running fasta_merge there should be a file:

 

[prefix].all.maker.augustus_masked.transcripts.fasta

 

in the output directory.  Is that what you need?

Mike

 

On Apr 6, 2013, at 9:25 AM, "Kang, Yang Jae" <kangyangjae at gmail.com> wrote:





Dear everyone!

 

I want to retrieve CDS sequences from the output of maker; however, in the augustus_masked feature there is no indication of CDS or Exon like maker features. Is there any way for me to retrieve CDS from augustus_masked? There were protein sequences in outdir but no CDS information.

 

Thank you!

 

Kang, Yang Jae

Ph.D.

Cropgenomics Lab.

College of Agriculture and Life Science

Seoul National University

Korea

 

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